The significant progress in the understanding of the molecular basis of human disease in the last few decades has led to a significant increase in the number of potential therapeutic targets. Over the years many drugs have been developed that target various biological processes such as enzymatic reactions and signal receptors. Among these, protein synthesis inhibitors represent a large potential class of molecular targets with importance that spans across many therapeutic areas, such as antibiotics, antivirals, and anticancer treatments.
One class of under utilized therapeutic targets is the ribonucleic acids (RNAs) involved in bacterial protein synthesis. More specifically, the protein synthesis processes that use post-transcriptional modified RNA nucleotides as substrates may be ideal therapeutic targets. Post-transcriptional nucleotide modifications can be as simple as the addition of a methyl group to a standard nucleotide or complex multi-step addition of amino acid like side chains (Soll, D. and RajBhandary, U. L., tRNA: Structure, Biosynthesis, and Function, ASM Press 1995; Grosjean, H. and Benne, R., Modification and Editing of RNA., Washington, D.C., ASM Press, 1998). While 1 to 2% of all RNA bases are modified, the nucleotides in the active sites of the ribosome and the transfer RNA (tRNA) that interact with the ribosome are modified at 10-fold the rate of modification outside these active sites. One of the functions of these modifications is to enhance the selectivity and specificity of the RNA:enzyme interactions that occur during transcription and translation. One such class of enzymes that utilize tRNA containing modified nucleotide bases is the amino acyl tRNA synthetases (AaRS) which catalyze the attachment of a specific amino acid to its corresponding tRNA. The specificity of the AaRS to their respective amino acid can be influenced by many features of the tRNA molecule including the modified nucleotide bases. In the case of the Lysine tRNA synthetase (LysRS), the anticodon stem loop (ASL) of the tRNA contains 2 or 3 modified nucleotide bases depending upon the organism.
There is a need for the identification of inhibitors of protein synthesis from RNA molecules having modified nucleotide bases. To this end, there also remains a need for the development of methods for the identification of such inhibitors. Such inhibitors may be useful for the development of, for example, antimicrobial compounds for use in therapeutic applications.